Ionic liquids (ILs) have been used in DNA extraction/separation, DNA preservation and PCR based on their characteristic affinity to DNA. However, few studies have been performed about how DNA-IL complex forms and its mechanism which would be essential to understand the role of ILs over the range of applications. Herein, we present that the differences in the structure of the DNA- IL complex are associated with the alkyl chain length of IL. The assumption was evidenced by Atomic force microscopy, DNA specific dye staining, gel-electrophoresis and real-time electrical measurement. We observed unique electrical signals with altered duration time and amplitude when DNA- ILs complexes pass through solid-state nanopore. We examined three types of ILs (EMIM-Cl, BMIM-Cl, and OMIM-Cl) for their characteristics to form DNA-ILs complexes. The results indicated that the length of hydrophobic alkyl group in respective ILs determines the form of DNA-IL complex. In conclusion, the morphology of DNA could be modified by the incorporation with different alkyl chain length of ILs, providing their further application in biosensor such as nanopore technique for DNA sequencing or understanding protein-DNA interaction.